As someone who has played nearly every shooter on every platform the past 10 years or so, I have to go with Unreal Engine. From Quake 3 and Unreal Tourney 2k4 to Gear of War 3, it has been consistently excellent.
My favorite recent use of it was in Space Marine, a game which stole one of my long-standing game design quests to incorporate melee fighting into a shooter properly. It was, of course, not the ideal solution but an admirable attempt and a vision into what games will look like in 10-20 years; where you won't be limited by concepts like shooter, rpg, open world, fighter, racer...the best games will incorporate all necessary methods in order to completely immerse you into the story, without being limited by a certain style of gameplay; and then they hopefully transfer that effort into the multiplayer portion as well as Space Marine did.
I would love to see someone really run with this idea like a Shadowrun tried to do, but of course the industry might be too stale to turn that corner for the next few years. Only time will tell, but it should be interesting to see what comes down the pipe the next decade or two.